CodonCode Aligner 5.0.1 was released on March 27, 2014. This version adds many new features, including support for alignments with Bowtie2, the option to display paired ends for Bowtie2 alignments in the contig view, support for Clustal Omega, improved gap editing, contig overview printing, and multiple speed and memory improvements for large projects. For more information, please visit www.codoncode.com/aligner/new.htm.

Version 5.0 requires a new license key. Version 5 is a free upgrade for all users with a current update and support agreement as of March 27, 2014. This includes all users who purchased a license within the past 12 months. Users qualifying for a free upgrade will receive a new license key by email. If you have questions about your license key or support agreement, or would like to provide feedback, please contact CodonCode's support team.